Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond

Deng, Min; Hou, Jie; Song, Kang; Chen, Jieyu; Gou, Jingwei; Li, Dapeng; He, Xinyi

doi:10.1016/j.aquaculture.2019.734911

Cited by 31 publications

(30 citation statements)

References 42 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…As a result, outside of extreme environments (e.g. saline/hypersaline [10][11][12], thermokarsts [13]), and aquaculture facilities [14][15][16] ponds remain largely understudied [17], especially with regard to their microbial communities.…”

Section: Introductionmentioning

confidence: 99%

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Chopyk

Nasko

Allard

et al. 2020

Environmental Microbiome

View full text Add to dashboard Cite

Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

show abstract

Section: Introductionmentioning

confidence: 99%

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Chopyk

Nasko

Allard

et al. 2020

Environmental Microbiome

View full text Add to dashboard Cite

show abstract

“…Despite this, our metagenomic analysis showed high genetic potential for ammonium assimilation within heterotrophic bacterial groups. Similar functional characteristics were reported in lakes (Rathour et al, 2020), aquaculture pond (Deng et al, 2020), soda lakes (Andreote et al, 2018), and streams (Reis et al, 2016).…”

Section: Discussionsupporting

confidence: 77%

“…Tanto as composições taxonômicas como as funcionais desses microrganismos parecem ser influenciadas pelas concentrações de nitrogênio disponíveis no ambiente (YANG et al 2019). Outros filos como, Actinobacteria, Bacteroidetes, Planctomycetes e Verrucomicrobia, são encontrados em ecossistemas aquáticos, e também apresentam potencial metabólico para participar de diferentes rotas do nitrogênio, incluindo desnitrificação, nitrificação, amonificação e até mesmo fixação de nitrogênio (MEDEIROS et al, 2016;ANDREOTE et al, 2018;DENG et al, 2020).…”

Section: O Fitoplâncton E Bacterioplâncton No Metabolismo Do Nitrogêniounclassified

“…However, recent studies have reported that heterotrophic bacteria can also contribute significantly to this process in temperate marine and estuary environments environments (Kirchman and Wheeler, 1998;Bradley et al, 2010;Yuan et al, 2012;Trottet et al, 2016), however there are few measurements in freshwater environments, especially in subtropical and tropical zones. Heterotrophic bacteria may also be involved in other metabolic pathways of N in aquatic environments, such as nitrification, ammonification, denitrification and nitrogen fixation (for cases of diazotrophic bacteria) Delmont., 20018;Deng et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…(Grossart et al, 2020). However, most of the available studies regarding taxonomy and functional roles of microorganisms are concentrated in temperate areas (Mohiuddin et al, 2017;Chopyk et al, 2020;Fasching et al, 2020;Llorens-Marès et al, 2020), with a limited number of researches carried out in tropical environments (Meneghine et al, 2017;Deng et al, 2020).…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Estudo do fitoplâncton e bacterioplâncton no metabolismo do nitrogênio em reservatórios subtropicais

Rodrigues¹

View full text Add to dashboard Cite

show abstract

Role of archaea in aquaculture: prospects and challenges

Jifiriya,

Preena,

Rejish Kumar

et al. 2023

Aquacult Int

View full text Add to dashboard Cite

Community metagenomic assembly reveals microbes that contribute to the vertical stratification of nitrogen cycling in an aquaculture pond

Cited by 31 publications

References 42 publications

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

Estudo do fitoplâncton e bacterioplâncton no metabolismo do nitrogênio em reservatórios subtropicais

Role of archaea in aquaculture: prospects and challenges

Contact Info

Product

Resources

About